7-55191757-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005228.5(EGFR):c.2508C>T(p.Arg836Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 1,613,938 control chromosomes in the GnomAD database, including 479 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005228.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGFR | ENST00000275493.7 | c.2508C>T | p.Arg836Arg | synonymous_variant | Exon 21 of 28 | 1 | NM_005228.5 | ENSP00000275493.2 | ||
EGFR | ENST00000455089.5 | c.2373C>T | p.Arg791Arg | synonymous_variant | Exon 20 of 26 | 1 | ENSP00000415559.1 | |||
EGFR | ENST00000450046.2 | c.2349C>T | p.Arg783Arg | synonymous_variant | Exon 21 of 28 | 4 | ENSP00000413354.2 | |||
EGFR | ENST00000700145.1 | c.855C>T | p.Arg285Arg | synonymous_variant | Exon 8 of 9 | ENSP00000514824.1 |
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2441AN: 152016Hom.: 34 Cov.: 32
GnomAD3 exomes AF: 0.0165 AC: 4153AN: 251218Hom.: 67 AF XY: 0.0166 AC XY: 2255AN XY: 135764
GnomAD4 exome AF: 0.0219 AC: 31945AN: 1461804Hom.: 446 Cov.: 31 AF XY: 0.0212 AC XY: 15445AN XY: 727208
GnomAD4 genome AF: 0.0160 AC: 2440AN: 152134Hom.: 33 Cov.: 32 AF XY: 0.0160 AC XY: 1190AN XY: 74368
ClinVar
Submissions by phenotype
not provided Benign:4
EGFR: BP4, BP7, BS1, BS2 -
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This variant is associated with the following publications: (PMID: 24899223, 22192147) -
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not specified Benign:2
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EGFR-related lung cancer Benign:1
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Lung cancer Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at